The hosts reached 87-2 in their second innings at the break, still 68 runs behind New Zealand's first innings total of 437 runs.
Tamim Iqbal was carrying the hopes of Bangladesh with 32 not out along side Mominul Haque, unbeaten on 20.
Wagner, who claimed 5-64 in the first innings, scalped opener Anamul Haque, caught by Peter Fulton at slip for 22 before the South African-born left-arm pacer added Marshall Ayub to his tally.
Anamul's highest score in the series included four boundaries.
Earlier New Zealand resumed their innings on 419-8 but added just 18 runs with their remaining two wickets.
Ish Sodhi was run out by Mominul for 58 before Abdur Razzak trapped Trent Boult in front to wrap up the innings seven overs into the morning session.